4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/inc/encode/encodePeak.h src/hg/inc/encode/encodePeak.h
index 78dc81c..d0492b2 100644
--- src/hg/inc/encode/encodePeak.h
+++ src/hg/inc/encode/encodePeak.h
@@ -1,124 +1,124 @@
 /* encodePeak.h was originally generated by the autoSql program, which also 
  * generated encodePeak.c and encodePeak.sql.  This header links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2008 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef ENCODEPEAK_H
 #define ENCODEPEAK_H
 
 #ifndef TRACKDB_H
 #include "trackDb.h"
 #endif
 
 #define ENCODEPEAK_NUM_COLS 13
 
 struct encodePeak
 /* Peaks format (BED 6+) */
     {
     struct encodePeak *next;  /* Next in singly linked list. */
     char *chrom;	/* Reference sequence chromosome or scaffold */
     unsigned chromStart;	/* Start position in chromosome */
     unsigned chromEnd;	/* End position in chromosome */
     char *name;	/* The name... probably just a period */
     unsigned score;	/* Score 1-1000 */
     char strand[3];	/* +, -, or . */
     float signalValue;	/* Measurement of average enrichment for the region */
     float pValue;	/* Statistical significance of signal value (-log10) */
     float qValue;	/* Statistical significance normalized/corrected across datasets. Use -1 if no qValue is assigned. */
     int peak;	/* Point-source called for this peak; 0-based offset from chromStart (use -1 if no point-source called) */
     unsigned blockCount;	/* Number of blocks */
     unsigned *blockSizes;	/* Comma separated list of block sizes */
     unsigned *blockStarts;	/* Start positions relative to chromStart */
     };
 
 struct encodePeak *encodePeakLoad(char **row);
 /* Load a encodePeak from row fetched with select * from encodePeak
  * from database.  Dispose of this with encodePeakFree(). */
 
 struct encodePeak *encodePeakLoadAll(char *fileName);
 /* Load all encodePeak from whitespace-separated file.
  * Dispose of this with encodePeakFreeList(). */
 
 struct encodePeak *encodePeakLoadAllByChar(char *fileName, char chopper);
 /* Load all encodePeak from chopper separated file.
  * Dispose of this with encodePeakFreeList(). */
 
 #define encodePeakLoadAllByTab(a) encodePeakLoadAllByChar(a, '\t');
 /* Load all encodePeak from tab separated file.
  * Dispose of this with encodePeakFreeList(). */
 
 struct encodePeak *encodePeakCommaIn(char **pS, struct encodePeak *ret);
 /* Create a encodePeak out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new encodePeak */
 
 void encodePeakFree(struct encodePeak **pEl);
 /* Free a single dynamically allocated encodePeak such as created
  * with encodePeakLoad(). */
 
 void encodePeakFreeList(struct encodePeak **pList);
 /* Free a list of dynamically allocated encodePeak's */
 
 void encodePeakOutput(struct encodePeak *el, FILE *f, char sep, char lastSep);
 /* Print out encodePeak.  Separate fields with sep. Follow last field with lastSep. */
 
 #define encodePeakTabOut(el,f) encodePeakOutput(el,f,'\t','\n');
 /* Print out encodePeak as a line in a tab-separated file. */
 
 #define encodePeakCommaOut(el,f) encodePeakOutput(el,f,',',',');
 /* Print out encodePeak as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 #define ENCODE_PEAK_KNOWN_FIELDS 15
 
 #define ENCODE_PEAK_NARROW_PEAK_FIELDS 10
 #define ENCODE_PEAK_BROAD_PEAK_FIELDS 9
 #define ENCODE_PEAK_GAPPED_PEAK_FIELDS 15
 
 /* Handy little enum for classification of the different peak types. */
 enum encodePeakType
 {
     invalid = 0,
     narrowPeak = 1,
     broadPeak = 2,
     gappedPeak = 3,
     encodePeak = 4,
 };
 
 enum encodePeakType encodePeakInferType(int numFields, char *type);
 /* Given a track type string and number of fields in a row, infer the type */
 
 int encodePeakNumFields(char *db, char *trackName);
 /* Just quickly count the number of fields. */
 
 enum encodePeakType encodePeakInferTypeFromTable(char *db, char *table, char *tdbType);
 /* Given the trackDb figure out the peak type. Returns zero on error. */ 
 
 struct encodePeak *encodePeakGeneralLoad(char **row, enum encodePeakType pt);
 /* Make a new encodePeak and return it. */
 
 struct encodePeak *narrowPeakLoad(char **row);
 /* Load a narrowPeak */
 
 struct encodePeak *broadPeakLoad(char **row);
 /* Load a broadPeak */
 
 struct encodePeak *gappedPeakLoad(char **row);
 /* Load a gappedPeak */
 
 struct encodePeak *encodePeakLineFileLoad(char **row, enum encodePeakType pt, struct lineFile *lf);
 /* From a linefile line, load an encodePeak row.  Errors outputted */
 /* have line numbers, etc. Does more error checking as well. */
 
 void encodePeakOutputWithType(struct encodePeak *el, enum encodePeakType pt, FILE *f);
 /* Print out encodePeak different ways depending on narrowPeak, broadPeak, etc. */
 /* but make it tab-separated. */
 
 #define ENCODE_PEAK_PVAL_FILTER_SUFFIX "pValFilter"
 #define ENCODE_PEAK_QVAL_FILTER_SUFFIX "qValFilter"
 #define ENCODE_PEAK_SCORE_FILTER_SUFFIX "scoreFilter"
 
 #endif /* ENCODEPEAK_H */